Tool&Dataset

Dataset and Software

■Dataset

PLISM: Large-scale histological image dataset toward stain and device-agnostic models.

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Project page: https://p024eb.github.io/
Paper:

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SegPath : The largest-scale datasets for the segmentation of cancer histology images

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Project page: https://dakomura.github.io/SegPath/
Paper: https://www.cell.com/patterns/fulltext/S2666-3899(23)00019-3

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Stomach Encyclopedia: Single-Cell and Spatial Transcriptome dataset of Human Stomach

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Dataset:
Paper:

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Histology images from uniform tumor regions in TCGA Whole Slide Images

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Dataset: https://zenodo.org/record/5889558
Paper: https://www.sciencedirect.com/science/article/pii/S2211124722001486

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■Software

Luigi: Large Scale HistoPathological Image Retrieval System

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Link: https://luigi-pathology.com/
Paper: https://www.sciencedirect.com/science/article/pii/S2211124722001486

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Luigi (iOS version)

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Link: https://apps.apple.com/jp/app/luigi/id1246638302
Paper: https://www.sciencedirect.com/science/article/pii/S2211124722001486

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deeptexture: Tools for deep texture representation for histology images

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Github: https://github.com/dakomura/deep_texture_histology
Document: https://deep-texture-histology.readthedocs.io/en/latest/
Paper: https://star-protocols.cell.com/protocols/2546

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Viola: a structural variant signature extractor with user-defined classifications

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Github: https://github.com/dermasugita/Viola-SV
Document: https://viola-sv.readthedocs.io/en/1.0.x-stable-doc/
Paper: https://academic.oup.com/bioinformatics/article/38/2/540/6371863

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